The problem with judging the whole fight is that emotion would come into play over what actually happened. A fighter could have one flurry in the last round and have the judges sway their vote. All the while throwing out the previous 2 or 4 rounds.
What I would like to see, takedowns recieve a fraction of the points unless you advance position, or land significant gnp. If that were the case, Thompson may have won the fight. The takedowns Gilbert landed had a significant play in that decision i'm sure, when they didn't lead to much.